Fig. 5: UMAP dimensionality reduction with pathway-specific genes by disease status and genetic cohort. | npj Parkinson's Disease

Fig. 5: UMAP dimensionality reduction with pathway-specific genes by disease status and genetic cohort.

From: Decreased SNCA expression in whole-blood RNA analysis of Parkinson’s disease adjusting for neutrophils

Fig. 5

UMAP embeddings were created from VST gene counts. Counts were then corrected for participant age and sex, as well as sample mRNA percentage and predicted neutrophil percentage. a UMAP of 36 genes found in the ‘Parkinson’s Signaling Pathway’, with samples labeled by disease and genetic status, excluding samples from participants with unknown genetic status (n = 5470). Corresponding density plots were made, stratified by disease and genetic status. b A UMAP and set of density plots were created from 143 genes in the ‘Mitochondrial Dysfunction’ pathway (n = 5339). c A UMAP of 59 ‘BBSome Signaling Pathway’ genes and density plots (n = 5358). d UMAP and density plots of 52 ‘Leukocyte Extravasation Signaling Pathway’ genes (n = 5345). In b–d, a small cluster of ‘Healthy Control’ and ‘Idiopathic PD’ samples was removed for visualization purposes.

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